diff --git a/build.xml b/build.xml
index 01bc386ca..e0e25882a 100644
--- a/build.xml
+++ b/build.xml
@@ -77,7 +77,7 @@
-
+
diff --git a/lib/SysBio.jar b/lib/SysBio.jar
index 339509853..6446a65fb 100644
Binary files a/lib/SysBio.jar and b/lib/SysBio.jar differ
diff --git a/src/org/sbml/squeezer/SBMLsqueezer.java b/src/org/sbml/squeezer/SBMLsqueezer.java
index c57647321..3cb07ef33 100644
--- a/src/org/sbml/squeezer/SBMLsqueezer.java
+++ b/src/org/sbml/squeezer/SBMLsqueezer.java
@@ -42,8 +42,6 @@
import javax.xml.stream.XMLStreamException;
-import jp.sbi.garuda.platform.commons.exception.NetworkException;
-
import org.sbml.jsbml.Model;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.SBMLDocument;
@@ -68,9 +66,7 @@
import de.zbit.AppConf;
import de.zbit.Launcher;
import de.zbit.garuda.GarudaOptions;
-import de.zbit.garuda.GarudaSoftwareBackend;
import de.zbit.gui.GUIOptions;
-import de.zbit.gui.GUITools;
import de.zbit.io.FileWalker;
import de.zbit.io.filefilter.SBFileFilter;
import de.zbit.util.ResourceManager;
@@ -94,25 +90,29 @@
@SuppressWarnings("unchecked")
public class SBMLsqueezer extends Launcher {
+ private static Boolean libSBMLAvailable = null;
/**
- * Localization support.
+ * The {@link Logger} for this class.
*/
- public static final transient ResourceBundle MESSAGES = ResourceManager.getBundle(Bundles.MESSAGES);
+ private static final transient Logger logger = Logger.getLogger(SBMLsqueezer.class.getName());
+
/**
* Localization support.
*/
- public static final transient ResourceBundle WARNINGS = ResourceManager.getBundle(Bundles.WARNINGS);
+ public static final transient ResourceBundle MESSAGES = ResourceManager.getBundle(Bundles.MESSAGES);
- /**
- * The {@link Logger} for this class.
- */
- private static final transient Logger logger = Logger.getLogger(SBMLsqueezer.class.getName());
+ private static boolean sabiorkEnabled = true;
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 8751196023375780898L;
+ /**
+ * Localization support.
+ */
+ public static final transient ResourceBundle WARNINGS = ResourceManager.getBundle(Bundles.WARNINGS);
+
/**
*
* @return
@@ -121,22 +121,6 @@ public static List> getInteractiveConfigOptions() {
return Arrays.asList(getInteractiveConfigOptionsArray());
}
- private static boolean sabiorkEnabled = true;
-
- /**
- * @return the sabiorkEnabled
- */
- public static boolean isSABIORKEnabled() {
- return sabiorkEnabled;
- }
-
- /**
- * @param sabiorkEnabled the sabiorkEnabled to set
- */
- public static void setSABIORKEnabled(boolean sabiorkEnabled) {
- SBMLsqueezer.sabiorkEnabled = sabiorkEnabled;
- }
-
/**
*
* @return
@@ -178,42 +162,11 @@ public static String[] getPossibleEnzymeTypes() {
return enzymeTypes.toArray(new String[] {});
}
- private static Boolean libSBMLAvailable = null;
-
/**
- * Does initialization for creating a SBMLsqueezer Object.
- * Checks if libSBML is available and initializes the Reader/Writer.
- * @param tryLoadingLibSBML
- * @param reader
- * @param writer
+ * @return the sabiorkEnabled
*/
- private void initializeReaderAndWriter(boolean tryLoadingLibSBML) {
- if (tryLoadingLibSBML) {
- if (libSBMLAvailable == null) {
- try {
- // In order to initialize libSBML, check the java.library.path.
- System.loadLibrary("sbmlj");
- // Extra check to be sure we have access to libSBML:
- Class.forName("org.sbml.libsbml.libsbml");
- logger.info(MESSAGES.getString("LOADING_LIBSBML"));
- libSBMLAvailable = Boolean.TRUE;
- } catch (Error e) {
- libSBMLAvailable = Boolean.FALSE;
- } catch (Throwable e) {
- libSBMLAvailable = Boolean.FALSE;
- }
- }
- if (libSBMLAvailable.booleanValue()) {
- logger.info(MESSAGES.getString("LAUNCHING_LIBSBML"));
- sbmlIo = (SBMLio) new SBMLio(
- new LibSBMLReader(), new LibSBMLWriter());
- }
- }
- if (sbmlIo == null) {
- logger.info(MESSAGES.getString("LOADING_JSBML"));
- sbmlIo = (SBMLio) new SBMLio(new SqSBMLReader(),
- new SqSBMLWriter());
- }
+ public static boolean isSABIORKEnabled() {
+ return sabiorkEnabled;
}
/**
@@ -225,15 +178,22 @@ public static void main(String[] args) {
}
/**
- *
+ * @param sabiorkEnabled the sabiorkEnabled to set
*/
- private SBMLio sbmlIo;
+ public static void setSABIORKEnabled(boolean sabiorkEnabled) {
+ SBMLsqueezer.sabiorkEnabled = sabiorkEnabled;
+ }
/**
*
*/
private AppConf appConf;
+ /**
+ *
+ */
+ private SBMLio sbmlIo;
+
/**
*
*/
@@ -262,6 +222,7 @@ public SBMLsqueezer(SBMLInputConverter sbmlReader,
*/
public SBMLsqueezer(String[] args) {
super(args);
+ System.out.println(getId());
}
/* (non-Javadoc)
@@ -323,7 +284,6 @@ public List> getCmdLineOptions() {
return list;
}
-
/* (non-Javadoc)
* @see de.zbit.Launcher#getInteractiveOptions()
*/
@@ -332,6 +292,7 @@ public List> getInteractiveOptions() {
return getInteractiveConfigOptions();
}
+
/* (non-Javadoc)
* @see de.zbit.Launcher#getLogPackages()
*/
@@ -381,7 +342,7 @@ public URL getURLOnlineUpdate() {
*/
@Override
public String getVersionNumber() {
- return "2.0";
+ return "2.0.1";
}
/* (non-Javadoc)
@@ -409,29 +370,51 @@ public java.awt.Window initGUI(AppConf appConf) {
if (properties.containsKey(IOOptions.SBML_IN_FILE)) {
readSBMLSource(properties.get(IOOptions.SBML_IN_FILE));
}
- final SBMLsqueezerUI gui = new SBMLsqueezerUI(getSBMLIO(), appConf);
- if (getCmdLineOptions().contains(GarudaOptions.class)
- && (!appConf.getCmdArgs().containsKey(GarudaOptions.CONNECT_TO_GARUDA) ||
- appConf.getCmdArgs().getBoolean(GarudaOptions.CONNECT_TO_GARUDA))) {
- new Thread(new Runnable() {
- /* (non-Javadoc)
- * @see java.lang.Runnable#run()
- */
- @Override
- public void run() {
- try {
- GarudaSoftwareBackend garudaBackend = new GarudaSoftwareBackend(
- "dd624b40-7bc0-11e2-b92a-0800200c9a66", gui);
- garudaBackend.init();
- } catch (NetworkException exc) {
- GUITools.showErrorMessage(gui, exc);
- } catch (Throwable exc) {
- logger.fine(getMessage(exc));
- }
+ return new SBMLsqueezerUI(getSBMLIO(), appConf);
+ }
+
+ /**
+ * Does initialization for creating a SBMLsqueezer Object.
+ * Checks if libSBML is available and initializes the Reader/Writer.
+ * @param tryLoadingLibSBML
+ * @param reader
+ * @param writer
+ */
+ private void initializeReaderAndWriter(boolean tryLoadingLibSBML) {
+ if (tryLoadingLibSBML) {
+ if (libSBMLAvailable == null) {
+ try {
+ // In order to initialize libSBML, check the java.library.path.
+ System.loadLibrary("sbmlj");
+ // Extra check to be sure we have access to libSBML:
+ Class.forName("org.sbml.libsbml.libsbml");
+ logger.info(MESSAGES.getString("LOADING_LIBSBML"));
+ libSBMLAvailable = Boolean.TRUE;
+ } catch (Error e) {
+ libSBMLAvailable = Boolean.FALSE;
+ } catch (Throwable e) {
+ libSBMLAvailable = Boolean.FALSE;
}
- }).start();
+ }
+ if (libSBMLAvailable.booleanValue()) {
+ logger.info(MESSAGES.getString("LAUNCHING_LIBSBML"));
+ sbmlIo = (SBMLio) new SBMLio(
+ new LibSBMLReader(), new LibSBMLWriter());
+ }
+ }
+ if (sbmlIo == null) {
+ logger.info(MESSAGES.getString("LOADING_JSBML"));
+ sbmlIo = (SBMLio) new SBMLio(new SqSBMLReader(),
+ new SqSBMLWriter());
}
- return gui;
+ }
+
+ /* (non-Javadoc)
+ * @see de.zbit.Launcher#isGarudaEnabled()
+ */
+ @Override
+ public boolean isGarudaEnabled() {
+ return true;
}
/**
@@ -594,39 +577,12 @@ public void squeeze(Object sbmlSource, String outfile, boolean searchSABIO) thro
}
/**
- * Convenient method that writes a LaTeX file from the given SBML source.
- *
- * @param sbmlInfile
- * @param latexFile
- * @throws IOException
- * @throws SBMLException
- * @throws XMLStreamException
+ * @param absolutePath
+ * @param outputPath
+ * @throws Throwable
*/
- public void toLaTeX(Object sbmlSource, String latexFile) throws IOException, SBMLException, XMLStreamException {
- readSBMLSource(sbmlSource);
- SBPreferences prefsIO = SBPreferences.getPreferencesFor(GUIOptions.class);
- String dir = prefsIO.get(GUIOptions.OPEN_DIR).toString();
- if (latexFile != null) {
- File out = new File(latexFile);
- if (SBFileFilter.createTeXFileFilter().accept(out)) {
- String path = out.getParent();
- if (!path.equals(dir)) {
- prefsIO.put(GUIOptions.OPEN_DIR, path);
- }
- if (!out.exists()) {
- long time = System.currentTimeMillis();
- logger.info(MESSAGES.getString("WRITING_LATEX_OUTPUT"));
- SBML2LaTeX.convert(sbmlIo.getSelectedModel(), out);
- logger.info(MessageFormat.format(
- MESSAGES.getString("DONE_IN_MS"), (System.currentTimeMillis() - time)) + "\n");
- }
- } else {
- logger.log(Level.WARNING, MessageFormat.format(
- WARNINGS.getString("INVALID_TEX_FILE"), latexFile) +"\n");
- }
- } else {
- logger.log(Level.WARNING, WARNINGS.getString("NO_TEX_FILE_PROVIDED"));
- }
+ public void squeeze(String absolutePath, String outputPath) throws Throwable {
+ squeeze(absolutePath, outputPath, false);
}
/**
@@ -777,12 +733,39 @@ public Set squeezeWithKineticsFromSABIORK(SBMLDocument sbmlDocument, b
}
/**
- * @param absolutePath
- * @param outputPath
- * @throws Throwable
+ * Convenient method that writes a LaTeX file from the given SBML source.
+ *
+ * @param sbmlInfile
+ * @param latexFile
+ * @throws IOException
+ * @throws SBMLException
+ * @throws XMLStreamException
*/
- public void squeeze(String absolutePath, String outputPath) throws Throwable {
- squeeze(absolutePath, outputPath, false);
+ public void toLaTeX(Object sbmlSource, String latexFile) throws IOException, SBMLException, XMLStreamException {
+ readSBMLSource(sbmlSource);
+ SBPreferences prefsIO = SBPreferences.getPreferencesFor(GUIOptions.class);
+ String dir = prefsIO.get(GUIOptions.OPEN_DIR).toString();
+ if (latexFile != null) {
+ File out = new File(latexFile);
+ if (SBFileFilter.createTeXFileFilter().accept(out)) {
+ String path = out.getParent();
+ if (!path.equals(dir)) {
+ prefsIO.put(GUIOptions.OPEN_DIR, path);
+ }
+ if (!out.exists()) {
+ long time = System.currentTimeMillis();
+ logger.info(MESSAGES.getString("WRITING_LATEX_OUTPUT"));
+ SBML2LaTeX.convert(sbmlIo.getSelectedModel(), out);
+ logger.info(MessageFormat.format(
+ MESSAGES.getString("DONE_IN_MS"), (System.currentTimeMillis() - time)) + "\n");
+ }
+ } else {
+ logger.log(Level.WARNING, MessageFormat.format(
+ WARNINGS.getString("INVALID_TEX_FILE"), latexFile) +"\n");
+ }
+ } else {
+ logger.log(Level.WARNING, WARNINGS.getString("NO_TEX_FILE_PROVIDED"));
+ }
}
}